[sphinx] Fixed baseline documentation

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.. _bob.bio.vein.baselines: .. _bob.bio.vein.baselines:
=============================== =============================
Executing Baseline Algorithms Executing Baseline Algorithms
=============================== =============================
The first thing you might want to do is to execute one of the vein
recognition algorithms that are implemented in ``bob.bio.vein``.
In this section we introduce the baselines available in this pakcage.
To execute one of then in the databases available just run the following command::
Running Baseline Experiments $ bob bio pipelines vanilla-biometrics [DATABASE_NAME] [BASELINE]
----------------------------
To run the baseline experiments, you can use the ``verify.py`` script by .. note::
just going to the console and typing: Both, `[DATABASE_NAME]` and `[BASELINE]` can be either python resources or
python files.
.. code-block:: sh Please, refer to :ref:`bob.bio.base <bob.bio.base>` for more information.
$ verify.py
This script is explained in more detail in :ref:`bob.bio.base.experiments`.
The ``verify.py --help`` option shows you, which other options you can
set.
Usually it is a good idea to have at least verbose level 2 (i.e., calling
``verify.py --verbose --verbose``, or the short version ``verify.py
-vv``).
.. note:: **Running in Parallel**
To run the experiments in parallel, you can define an SGE grid or local host
(multi-processing) configurations as explained in
:ref:`running_in_parallel`.
In short, to run in the Idiap SGE grid, you can simply add the ``--grid``
command line option, without parameters. To run experiments in parallel on
the local machine, simply add a ``--parallel <N>`` option, where ``<N>``
specifies the number of parallel jobs you want to execute.
Database setups and baselines are encoded using
:ref:`bob.bio.base.configuration-files`, all stored inside the package root, in
the directory ``bob/bio/vein/configurations``. Documentation for each resource
is available on the section :ref:`bob.bio.vein.resources`.
.. warning::
You **cannot** run experiments just by executing the command line
instructions described in this guide. You **need first** to procure yourself
the raw data files that correspond to *each* database used here in order to
correctly run experiments with those data. Biometric data is considered
private data and, under EU regulations, cannot be distributed without a
consent or license. You may consult our
:ref:`bob.bio.vein.resources.databases` resources section for checking
currently supported databases and accessing download links for the raw data
files.
Once the raw data files have been downloaded, particular attention should be
given to the directory locations of those. Unpack the databases carefully
and annotate the root directory where they have been unpacked.
Then, carefully read the *Databases* section of
:ref:`bob.bio.base.installation` on how to correctly setup the
``~/.bob_bio_databases.txt`` file.
Use the following keywords on the left side of the assignment (see
:ref:`bob.bio.vein.resources.databases`):
.. code-block:: text
[YOUR_VERAFINGER_DIRECTORY] = /complete/path/to/verafinger
[YOUR_UTFVP_DIRECTORY] = /complete/path/to/utfvp
[YOUR_FV3D_DIRECTORY] = /complete/path/to/fv3d
Notice it is rather important to use the strings as described above,
otherwise ``bob.bio.base`` will not be able to correctly load your images.
Once this step is done, you can proceed with the instructions below.
In the remainder of this section we introduce baseline experiments you can
readily run with this tool without further configuration. Baselines examplified
in this guide were published in [TVM14]_.
Repeated Line-Tracking with Miura Matching Repeated Line-Tracking with Miura Matching
...@@ -98,36 +31,23 @@ protocol, do the following: ...@@ -98,36 +31,23 @@ protocol, do the following:
.. code-block:: sh .. code-block:: sh
$ verify.py verafinger rlt -vv $ bob bio pipelines vanilla-biometrics verafinger rlt -vv -c
.. tip:: .. tip::
If you have more processing cores on your local machine and don't want to If you have more processing cores on your local machine and don't want to
submit your job for SGE execution, you can run it in parallel (using 4 submit your job for SGE execution, you can run it in parallel by adding the options ``-l local-parallel``.
parallel tasks) by adding the options ``--parallel=4 --nice=10``. **Before**
doing so, make sure the package gridtk_ is properly installed.
Optionally, you may use the ``parallel`` resource configuration which
already sets the number of parallel jobs to the number of hardware cores you
have installed on your machine (as with
:py:func:`multiprocessing.cpu_count`) and sets ``nice=10``. For example:
.. code-block:: sh .. code-block:: sh
$ verify.py verafinger rlt parallel -vv $ bob bio pipelines vanilla-biometrics verafinger rlt -vv -c -l local-parallel
To run on the Idiap SGE grid using our stock To run on the Idiap SGE grid use:
io-big-48-slots-4G-memory-enabled (see
:py:mod:`bob.bio.vein.configurations.gridio4g48`) configuration, use:
.. code-block:: sh .. code-block:: sh
$ verify.py verafinger rlt grid -vv $ bob bio pipelines vanilla-biometrics verafinger rlt -vv -c -l sge
You may also, optionally, use the configuration resource ``gridio4g48``,
which is just an alias of ``grid`` in this package.
This command line selects and runs the following implementations for the This command line selects and runs the following implementations for the
...@@ -172,7 +92,7 @@ protocol like above, do the following: ...@@ -172,7 +92,7 @@ protocol like above, do the following:
.. code-block:: sh .. code-block:: sh
$ verify.py verafinger mc -vv $ bob bio pipelines vanilla-biometrics verafinger mc -vv -c
This command line selects and runs the following implementations for the This command line selects and runs the following implementations for the
...@@ -213,7 +133,7 @@ protocol like above, do the following: ...@@ -213,7 +133,7 @@ protocol like above, do the following:
.. code-block:: sh .. code-block:: sh
$ verify.py verafinger wld -vv $ bob bio pipelines vanilla-biometrics verafinger wld -vv -c
This command line selects and runs the following implementations for the This command line selects and runs the following implementations for the
...@@ -326,7 +246,7 @@ Now, re-run the experiment using your modified database descriptor: ...@@ -326,7 +246,7 @@ Now, re-run the experiment using your modified database descriptor:
.. code-block:: sh .. code-block:: sh
$ verify.py ./verafinger_full.py wld -vv $ bob bio pipelines vanilla-biometrics ./verafinger_full.py wld -vv -c
Notice we replace the use of the registered configuration file named Notice we replace the use of the registered configuration file named
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